R Development Page

Contributed R Packages

Below is a list of all packages provided by project MPAgenomics.

Important note for package
binaries: R-Forge provides these binaries only for
the most recent version of R, but not for older
versions. In order to successfully install the
packages provided on R-Forge, you have to switch
to the most recent version of R or, alternatively,
install from the package sources (.tar.gz).

Packages

HDPenReg

High-Dimensional Penalized Regression

Algorithms for lasso and fused-lasso problems: implementation of
the lars algorithm for lasso and fusion penalization and EM-based
algorithms for (logistic) lasso and fused-lasso penalization.

Preprocess and analysis of genomic data. MPAgenomics
provides wrappers from commonly used packages to streamline their repeated
manipulation, offering an easy-to-use pipeline. The segmentation of
successive multiple profiles is performed with an automatic choice of
parameters involved in the wrapped packages. Considering multiple profiles
in the same time, MPAgenomics wraps efficient penalized regression methods
to select relevant markers associated with a given outcome.

Build status codes

0 - Current: the package is available for download. The corresponding package passed checks on the Linux and Windows platform without ERRORs.
1 - Scheduled for build: the package has been recognized by the build system and provided in the staging area.
2 - Building: the package has been sent to the build machines. It will be built and checked using the latest patched version of R. Note that it is included in a batch of several packages. Thus, this process will take some time to finish.
3 - Failed to build: the package failed to build or did not pass the checks on the Linux and/or Windows platform. It is not made available since it does not meet the policies.
4 - Conflicts: two or more packages of the same name exist. None of them will be built. Maintainers are asked to negotiate further actions.
5 - Offline: the package is not available. The build system may be offline or the package maintainer did not trigger a rebuild (done e.g., via committing to the package repository).